modules/genomad_endtoend

Identify mobile genetic elements present in genomic assemblies

metagenomicsgenomaddatabasedownloadphagevirusplasmid

https://github.com/nf-core/modules/[...]/modules/nf-core/genomad/endtoend

Description

Identify mobile genetic elements present in genomic assemblies

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`fasta`
`:file`

FASTA file containing contigs/scaffolds/chromosomes

*.{fasta,fna,fa}

`meta2`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`genomad_db`
`:directory`

Directory pointing to geNomad database

Output

name:type

description

pattern

`genomad_results`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/`
`:file`

The full output directory from Genomad

${prefix}/

`aggregated_classification`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/_aggregated_classification/_aggregated_classification.tsv`
`:file`

Combined classification scores for each contig/scaffold/chromosome

*_aggregated_classification.tsv

`marker_classification`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/_marker_classification/_marker_classification.tsv`
`:file`

Marker-based classification scores when –disable-nn-classification is used

*_marker_classification.tsv

`taxonomy`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/_annotate/_taxonomy.tsv`
`:file`

Detailed output of geNomad’s marker gene taxonomy analysis

*_taxonomy.tsv

`provirus`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/_find_proviruses/_provirus.tsv`
`:file`

Detailed output of each provirus identified by geNomad’s find_proviruses module

*_provirus.tsv

`compositions`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/_score_calibration/_compositions.tsv`
`:file`

OPTIONAL - Predicted sample composition when --enable-score-calibration is used

*_compositions.tsv

`calibrated_classification`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/_score_calibration/_calibrated_aggregated_classification.tsv`
`:file`

OPTIONAL - Classification scores that have been adjusted based on sample composition when --enable-score-calibration is used`

*_calibrated_aggregated_classification.tsv

`plasmid_fasta`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/_summary/_plasmid.fna.gz`
`:file`

FASTA file containing predicted plasmid sequences

*_plasmid.fna

`plasmid_genes`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/_summary/_plasmid_genes.tsv`
`:file`

TSV file containing predicted plasmid genes and their annotations

*_plasmid_genes.tsv

`plasmid_proteins`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/_summary/_plasmid_proteins.faa.gz`
`:file`

FASTA file containing predicted plasmid protein sequences

*_plasmid_proteins.faa

`plasmid_summary`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/_summary/_plasmid_summary.tsv`
`:file`

TSV file containing a summary of geNomad’s plasmid predictions

*_plasmid_summary.tsv

`virus_fasta`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/_summary/_virus.fna.gz`
`:file`

FASTA file containing predicted virus sequences

*_virus.fna

`virus_genes`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/_summary/_virus_genes.tsv`
`:file`

TSV file containing predicted virus genes and their annotations

*_virus_genes.tsv

`virus_proteins`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/_summary/_virus_proteins.faa.gz`
`:file`

FASTA file containing predicted virus protein sequences

*_virus_proteins.faa

`virus_summary`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/_summary/_virus_summary.tsv`
`:file`

TSV file containing a summary of geNomad’s virus predictions

*_virus_summary.tsv

`versions_genomad`

`${task.process}`
`:string`

The name of the process

`genomad`
`:string`

The name of the tool

`genomad --version 2>&1 | sed 's/^.geNomad, version //; s/ .//'`
`:eval`

The expression to obtain the version of the tool

`versions_genomad_db`

`${task.process}`
`:string`

The name of the process

`genomad_db`
`:string`

The name of the tool

`if [ -s ${genomad_db}/version.txt ]; then cat ${genomad_db}/version.txt; else echo 'unknown'; fi`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`genomad`
`:string`

The name of the tool

`genomad --version 2>&1 | sed 's/^.geNomad, version //; s/ .//'`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`genomad_db`
`:string`

The name of the tool

`if [ -s ${genomad_db}/version.txt ]; then cat ${genomad_db}/version.txt; else echo 'unknown'; fi`
`:eval`

The expression to obtain the version of the tool

Tools

genomad
Lawrence Berkeley National Labs BSD variant license

Identification of mobile genetic elements

portal.nersc.gov/genomad https://github.com/apcamargo/genomad/ 10.1101/2023.03.05.531206

modules/genomad_endtoend

Description

Input

meta :map

fasta :file

meta2 :map

genomad_db :directory

Output

genomad_results

meta :map

${prefix}/ :file

aggregated_classification

meta :map

${prefix}/*_aggregated_classification/*_aggregated_classification.tsv :file

marker_classification

meta :map

${prefix}/*_marker_classification/*_marker_classification.tsv :file

taxonomy

meta :map

${prefix}/*_annotate/*_taxonomy.tsv :file

provirus

meta :map

${prefix}/*_find_proviruses/*_provirus.tsv :file

compositions

meta :map

${prefix}/*_score_calibration/*_compositions.tsv :file

calibrated_classification

meta :map

${prefix}/*_score_calibration/*_calibrated_aggregated_classification.tsv :file

plasmid_fasta

meta :map

${prefix}/*_summary/*_plasmid.fna.gz :file

plasmid_genes

meta :map

${prefix}/*_summary/*_plasmid_genes.tsv :file

plasmid_proteins

meta :map

${prefix}/*_summary/*_plasmid_proteins.faa.gz :file

plasmid_summary

meta :map

${prefix}/*_summary/*_plasmid_summary.tsv :file

virus_fasta

meta :map

${prefix}/*_summary/*_virus.fna.gz :file

virus_genes

meta :map

${prefix}/*_summary/*_virus_genes.tsv :file

virus_proteins

meta :map

${prefix}/*_summary/*_virus_proteins.faa.gz :file

virus_summary

meta :map

${prefix}/*_summary/*_virus_summary.tsv :file

versions_genomad

${task.process} :string

genomad :string

genomad --version 2>&1 | sed 's/^.*geNomad, version //; s/ .*//' :eval

versions_genomad_db

${task.process} :string

genomad_db :string

if [ -s ${genomad_db}/version.txt ]; then cat ${genomad_db}/version.txt; else echo 'unknown'; fi :eval

Topics

versions

${task.process} :string

genomad :string

genomad --version 2>&1 | sed 's/^.*geNomad, version //; s/ .*//' :eval

${task.process} :string

genomad_db :string

if [ -s ${genomad_db}/version.txt ]; then cat ${genomad_db}/version.txt; else echo 'unknown'; fi :eval

Tools

genomadLawrence Berkeley National Labs BSD variant license

included in

maintainers

get in touch

`meta`
`:map`

`fasta`
`:file`

`meta2`
`:map`

`genomad_db`
`:directory`

`genomad_results`

`meta`
`:map`

`${prefix}/`
`:file`

`aggregated_classification`

`meta`
`:map`

`${prefix}/_aggregated_classification/_aggregated_classification.tsv`
`:file`

`marker_classification`

`meta`
`:map`

`${prefix}/_marker_classification/_marker_classification.tsv`
`:file`

`taxonomy`

`meta`
`:map`

`${prefix}/_annotate/_taxonomy.tsv`
`:file`

`provirus`

`meta`
`:map`

`${prefix}/_find_proviruses/_provirus.tsv`
`:file`

`compositions`

`meta`
`:map`

`${prefix}/_score_calibration/_compositions.tsv`
`:file`

`calibrated_classification`

`meta`
`:map`

`${prefix}/_score_calibration/_calibrated_aggregated_classification.tsv`
`:file`

`plasmid_fasta`

`meta`
`:map`

`${prefix}/_summary/_plasmid.fna.gz`
`:file`

`plasmid_genes`

`meta`
`:map`

`${prefix}/_summary/_plasmid_genes.tsv`
`:file`

`plasmid_proteins`

`meta`
`:map`

`${prefix}/_summary/_plasmid_proteins.faa.gz`
`:file`

`plasmid_summary`

`meta`
`:map`

`${prefix}/_summary/_plasmid_summary.tsv`
`:file`

`virus_fasta`

`meta`
`:map`

`${prefix}/_summary/_virus.fna.gz`
`:file`

`virus_genes`

`meta`
`:map`

`${prefix}/_summary/_virus_genes.tsv`
`:file`

`virus_proteins`

`meta`
`:map`

`${prefix}/_summary/_virus_proteins.faa.gz`
`:file`

`virus_summary`

`meta`
`:map`

`${prefix}/_summary/_virus_summary.tsv`
`:file`

`versions_genomad`

`${task.process}`
`:string`

`genomad`
`:string`

`genomad --version 2>&1 | sed 's/^.geNomad, version //; s/ .//'`
`:eval`

`versions_genomad_db`

`${task.process}`
`:string`

`genomad_db`
`:string`

`if [ -s ${genomad_db}/version.txt ]; then cat ${genomad_db}/version.txt; else echo 'unknown'; fi`
`:eval`

`versions`

`${task.process}`
`:string`

`genomad`
`:string`

`genomad --version 2>&1 | sed 's/^.geNomad, version //; s/ .//'`
`:eval`

`${task.process}`
`:string`

`genomad_db`
`:string`

`if [ -s ${genomad_db}/version.txt ]; then cat ${genomad_db}/version.txt; else echo 'unknown'; fi`
`:eval`

genomad
Lawrence Berkeley National Labs BSD variant license